Posts by Matthew Thornton

... Hello!
My question is about reads that don't align to the genome yet are long and have very good Phred scores. Currently, my workflow is FastQC > Cutadapt > Trimmomatic > RNA-STAR > HTSeq-count > edgeR (RUVSeq) I use gencode genomes with Ensembl IDs and even with the cleanest isolati ...

... Thank you for the suggestions! I will look at where the ERCC controls
fall in the data. I am thinking to use a paired-down set of the ERCC
controls in the 'linear' range and which are within my experimental
data. I am planning to use the spike-in probes procedure in the vsn
package. I will also try ...

... Hello!
I am processing Affymetrix gene chip Rat Gene 2.0 ST chips with
bioconductor package xps using rma normalization. I have included the
ExFold ERCC external RNA controls with 2 mixes of different
concentrations. I am able to pull out intensities for the ERCC
controls at different points along ...

... Hello!
I am trying to optimize my data processing based on the addition of
ExFold ERCC controls. Ideally I would like to normalize with VSN using
the procedure in chapter 7 of the vsn vignette. If I pull out the
unprocessed intensities for the ERCC controls, order them by
increasing concentration, ...

... Hello!
I have some RNASeq data that I am analyzing with edgeR and I would
like to use the cqn package to correct for GC bias. I have aligned
the data to the UCSC hg38 genome.
>From googling I have found the the bedtools 'nuc' command will give
me the GC content with ranges and the length. Prov ...

... Hello!
I am using the vsn package to process Rat Gene 2.0 ST chips. I have to
export the data from xps and put the data into vsn as a matrix. The
data going into vsn has column names corresponding to "X" and "Y"
locations and the MEAN intensity for each sample.
I call vsn with ' fit <- vsn2(as. ...

... Hello!
I am digging through the control intensities for technical replicates
obtained with an Affymetrix GeneChip Rat Gene 2.0 ST array.
I have 3 technical replicates of the same sample. The kernel density
plot overlay of the raw data shows differences in the intensity
distributions.
When I pull ...

... Hi James,
Thank you for your reply!
> Not really. This is the point at which I start the experimental
design
grilling session. Why did you do the combination treatment? What did
you
expect to see (e.g., what is your hypothesis that you are testing)?
Yes, we are expecting synergy between the tr ...

... Hi Dario!
Thank you for your reply. I am glad that I have a proper design
matrix. I will try the 'Group1 -Group2 -Group3 + Control'
contrasts.matrix. I am not very experienced with general linear
models. So let me guess why that would be an appropriate contrast
matrix, is it because the null hypoth ...